Questions tagged [rna]

RNA, or ribonucleic acid, is a biological macromolecule made of nucleotides used in cells to convey genetic information to protein. RNA also plays a role in catalyzing certain biological reactions as well as carrying genetic material in some viruses.

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457 views

How do aminoacyl-tRNA synthases distinguish between similar amino acids?

How do aminoacyl tRNA synthases recognize the right amino acid for their tRNA? What is the structural reason behind the selective recognition? I have difficulty in seeing how, for example, leucine and ...
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Why is an initiator tRNA required, distinct from the methionine tRNA used in elongation?

I'm confused by why there is a need for different tRNA-methionine complexes for translational initiation and elongation. This paper mentions that It is important that each type of methionyl tRNA ...
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Longest transcripts without isoforms

Does anyone know what genes produce the longest mRNAs? I am planning a project on synthetic introns and want to use stuffer fragments to vary intron size. Obviously they must not contain any splicing ...
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Basic molecular biology of nucleic acids book for a mathematician studying DNA and RNA formally?

I am a mathematician studying DNA and RNA language from the perspective of Formal Language Theory. Note that I am aware of these posts: best book for a comprehensive introduction to biology for a ...
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154 views

Is it possible to produce a tangible mass of DNA/RNA using a PCR reaction?

A Polymerase Chain Reaction (PCR) is a method of amplification which enables one to produce many copies of a certain DNA/RNA strand for many applications (as described in the link above). I have ...
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Splicing and “the dominance of RNA-world”

This is a paragraph from my textbook. The significance of such complexities is now beginning to be understood. The split-gene arrangements represent probably an ancient feature of the genome. ...
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1answer
252 views

Which are the best programs to analyze circular RNA?

Hello I'm just started with bioinformatics and I would like to know which programs are best for the task of finding circRNA (circular RNA) in sequences of tissues and different cellular types. I have ...
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1answer
410 views

Functions of tracrRNA and crRNA in the CRISPR/Cas9 system

I need some help about Crispr / Cas9. The CRISPR/Cas9 technic consists (for bacterias) in "cut" bacteriophage's DNA, in order to make it unfunctional. When the RNA is transcribed (RNA which is ...
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RNA isolation problem

I have isolated RNA from cell culture (T25 flask, mouse cells) with trizol. I've measured the sample on Nanodrop, and this is what I've got: A260 (10mm): 16.408 A260/A280: 1.98 656.3 ng/ul How is this ...
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Why is uracil, rather than thymine, used in RNA?

This question was posed on SE Biology some time ago, but all the answers, including the accepted one, answered a different question instead: “Why is thymine, rather than uracil, used in DNA?”. I ...
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Can a ribozyme be present on two different RNA molecules?

Suppose we have a ribozyme that consists of an 'enzyme' strand and a 'substrate' strand. (e.g. hammerhead ribozyme) Is it possible to have the enzyme strand of the ribozyme on one RNA molecule and ...
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Translation of RNA into proteins

What's the least number of tRNA molecules needed to form a polypeptide chain that contain 50 amino acids of 15 types? I know that each type of amino acid has at least one unique type of tRNA that ...
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Why is thymine not incorporated into mRNA?

I am aware that in transcription uracil bonds to adenine and not thymine. But what is it that actually prevents thymine from bonding to adenine in transcription, that is not present in replication?
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non-coding RNA modelling in silico

I've been trying to model a non-coding RNA molecule which binds to a RNA binding protein. I found the DNA sequence for ncRNA from NCBI. I did not find the RNA seq of the same. Hence my doubt is, ...
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Annotation for non-model organism [closed]

I want to annotate data while analyzing transcritpome data using DESeq2 , usually Biomart R-package (https://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) does the needful , but for ...
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1answer
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Pyrimidine bases + genetic variation [closed]

I don't understand this question, hoping someone can help! One of the following bases does not belong among pyrimidine bases: - Uracil - Adenine - Cytosine - Thymine I thought that everyone ...
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Confusion about the role of capping and polyadenylation in nuclear transport

Before termination stage of transcription a GMP cap is added to the 5' end and poly-A tail to 3' end of mRNA. The link(http://sciencing.com/role-rna-polyadenylation-5434666.html) says: The poly(A) ...
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Modifications of free nucleotides

We know that RNA can get modified post transcriptionally (RNA modification). So when the RNA is degraded, is it possible for such modifications to still be present on the individual nucleotides -- ...
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RNA isolation- role of pH

Why does RNA alone go into the aqueous phase when treated with phenol-chloroform at lower pH? At a neutral or basic pH, both DNA and RNA would escape into the aqueous phase. So how is DNA held back at ...
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1answer
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Why is the ribonucleoside derived from thymine, 5-Methyluridine, abbreviated m5U and not T?

The wikipedia article about Nucleosides presents a table in which there are three columns — Base, Ribonucleoside and Deoxyribonucleoside — and structures, names and abbreviations for the nucleosides ...
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Validity of comparing gene expression levels between alive and <24h postmortem cohort

There is a recent paper about assessment of a suicidal risk in psychotic patients https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759104/ One of the important points is that the authors compare gene ...
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What is sense RNA?

I heard my professor use this term.He said that it is a RNA that has the sense of synthesising the protein. But there's no authentic online source to verify it, except this one (biology-pages.info) ...
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How often does pre-mRNA processing lead to midstream off-frame errors in eukaryotic mRNAs?

As I understand it, the splicing of introns from pre-mRNAs is not incredibly precise. I've only ever seen nucleotide position ranges given in any description of the involved processes. Since there is ...
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Do any RNAs directly inhibit transcription

In eukaryotes, microRNAs and small interfering RNAs, as part of protein complexes, can attack specific messenger RNAs with complementary sequences, thereby inhibiting translation. However, RNA can ...
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449 views

Why was not RNA completely replaced by DNA when the RNA world evolved into a DNA and protein world?

If DNA just has a slightly different chemical composition from RNA, why can't DNA act as a catalyst and why hasn't it replaced RNA? Here, I am talking in terms of evolution, shouldn't evolution just ...
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How many proteins do all human ribosomes together produce per hour? [closed]

Very roughly how many proteins (chains) are synthesized in the human body per hour under normal conditions? (And how many ribosomes does the human body have?)
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What is RNA Engineering

I've been hearing the term passed around, and my own research has led me to some very high-level papers which propose new tools for accomplishing RNA engineering. From the abstract of one of the ...
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1answer
183 views

RT-qPCR for RNA quantification

I'm really new to RT-qPCR and probably I've just a minor problem than I think. So, what's my problem about. I want to quantify a virus by a specific area within a gene on its genome. I've specific ...
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Travelling with tissue samples in RNAlater

I've been in Brazil collecting some samples (ants) and need to travel back to to the UK with - I've got their brains stored in RNAlater, which have been in the freezer at -4C for a bit less than a ...
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2answers
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Spectrophotometric Values of Individual Nucleotides

All around the net you will find this list giving 260/280 ratios of individual nucleotides: Guanine: 1.15 Adenine: 4.50 Cytosine: 1.51 Uracil: 4.00 Thymine: 1.47 Yet I cannot find a reliable source ...
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What stops messenger RNA from binding to itself?

Since mRNA is single-stranded, and (mostly) floats freely within the cytosol, what stops it from folding onto itself (like DNA) and preventing transcription?
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How to determine continental ancestry group (race) with transcriptome data obtained with RNA microarray?

Say I have a whole genome expression data (transcriptome) for some sampled human tissue. Is this data sufficient to find out the continental ancestry group of a donor?
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Can the “Cas9”(involved on the Crispr-cas9 mechanism) be considered as a restriction enzyme?

I have many questions about the Cas9 enzyme. When the Cas9-guideRNA (crRNA and transcrRNA) complex is attached to the DNA sequence, what is the type of bond that cuts the Cas9? Does the Cas9 degrade ...
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Chemistry of the phosphodiester bond in RNA

I have been learning about the chemical structure of RNA, but I can't understand why all hydrogen atoms disappear in the phosophodiester bond between the riboses of RNA. Phosphoric acid is $H_3PO_4$: ...
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1answer
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miRNA analysis just using BLAST against mirbase.org

I have sequencing data (Illumina). Library prep was focused on short ncRNAs. I would like to identify human miRNAs. Do you think it is feasible to simply BLAST ...
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1answer
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What is the gene corresponding to MIR382 RNA molecule? [closed]

Where can I find information such as this?
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2answers
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How can there be a one-to-one correspondence between RNA and genes?

From what I know, multiple strands of DNA make up a gene, so how can for each gene there can only be one RNA corresponding to it and vice versa? Is my knowledge incorrect?
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Does tRNA contain parts with double-helix structure? [closed]

I read in some place that tRNA has a part which is double-stranded. I wanted to know if that part is similar to DNA (double-helix). (And I know that tRNA won't contain Thymine)
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1answer
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Can RNA be extracted from tissue suspended in formalin?

There are two tumor samples floating in a 10% formaldehyde solution (i.e formalin). Is there a protocol for RNA extraction under these circumstances? I am concerned that using the protocol for ...
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1answer
669 views

What is the transcriptome in layman's term?

I am new to the bioinformatics field and am trying to understand a research paper that includes some terminology without definitions. The term transcriptome in particular is banded around in the ...
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To what extent is the genetic code more than just a code?

It is worth specifying the exact meaning of "code" in this question. A code is a map from one space to another space with which it has no algorithmic connection. Thus representing 321 as 0x141 is not ...
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Why is tRNA called an adaptor molecule?

All I know about adaptor is that it is a device that converts attributes of one electrical device or system to those of an otherwise incompatible device or system. Thank you.
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Estimating RNA concentration from Specific Activity of Labeled RNA

The question reads, Using T7 RNA polymerase to transcribe in vitro a 100-nt RNA off a DNA template. This RNA contains 19 Adenosines. In your 100 uL transcription reaction you added 1.00 µL of α32P•[...
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1answer
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Can ncRNA convert to coding RNA/mRNA by mutations?

DNA has transcribed into RNA (Non-coding). Can this RNA mutate and become a Protein-Coding one/mRNA? Have there been any such instances reported by scientists?
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What is meant by “Expression” of Non-Coding RNA?

I was having a look at lncRNAdb and its help says: The ENCODE project gene annotation list, GENCODE, has predicted that the human genome contains 14,470 lncRNAs whereas only a small proportion of ...
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Do transcripts always start and end with exons?

I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or ...
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249 views

Why is statistical mechanics relevant to RNA and protein folding?

This is a very naive question. As far as I understand the folding of a molecule is governed by the electromagnetic forces between its atoms and also between its atoms and the atoms in the surrounding ...
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Is there any virus that contains both DNA and RNA in its genome?

It is known that viruses contain DNA or RNA- either one and not both. I came across a question: Which virus contains both DNA and RNA?
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What's the difference between CREs and DHSs?

I would like to know what's the difference between cis-regulating elements and DNase I–hypersensitive sites, in order to produce a meaningful segregation of non coding elements affecting gene ...
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Why do RNAi pathway proteins exist in the nematode when they can cause them harm?

When dsRNA is injected in plant, Dicer cuts it and prevents disease. Why would the plant parasite, M. incognita - a nematode, die when dsRNA was injected in it? It should have saved it. Again, to be ...

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